FarSight Studios just posted this to their Facebook page:

There is a known issue with the Android update. It could potentially wipe out some users' save file; deleting goals and local high scores. Note this will not effect purchases or leaderboards. We will address this so that future updates don't wipe your save data. We apologize for the inconvenience.
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It may be a good idea to skip this update, if you haven't already installed it.

Update: This issue has been fixed with the 1.0.3 update, now available.